Events

Current tools in structural biology

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This evening seminar/workshop will focus on current developments within structural biology. We are delighted to announce that you will be joined by Phd. Chris W Woods from University of Bristol, whose work with parametric solutions to protein design and modelling have recently been published (Oct. 2017) under the acronym ISAMBARD. ISAMBARD is a strong contender to Prof. David Baker's Rosetta, and is especially suitable for modelling of alpha-helixes, which is implemented in CCbuilder2.0, also recently published (Aug. 2017).

Our second speaker, Christian Munk. is a Phd fellow from the institute of phamacology (UCPH), and he will present his recent work on categorizing and m...odelling G-protein coupled receptors (GPCRs). For this purpose, Christian and colleagues from the group of Ass. Prof. David Gloriam contributed to GPCRdb, which provide data and analysis tools for the wider GPCR-community - allowing for structural explanations to pharmacological issues.

Program:
17.30 Welcome by CBioVikings

17.45 Phd. Chris W. Woods. University of Bristol.
ISAMBARD an open-source computational environment for biomolecular analysis, modelling and design.

19.15 Break and refreshments

19.30 Phd. fellow Christian Munk, University of Copenhagen.
GPCRdb: The G-coupled receptor database - an introduction.

21:00 End of workshop

Chris and Christian will be giving a talk on ISAMBARD and GPCRdb respectively, and will be bringing a set of introductory exercises for you to get a "hands on experience". We therefore recommend you to have the following programs and packages ready to use on the evening:
- Python
- (PC users) Visual studio with visual C++ tools (https://www.visualstudio.com/vs/cplusplus/)
- ISAMBARD (https://github.com/woolfson-group)
- (optional) SCWRL4 (http://dunbrack.fccc.edu/scwrl4/)
- (optional) DSSP (http://swift.cmbi.ru.nl/gv/dssp/)

For more information, I emplore you to have a look at our synopsis for the events (posted below), or seek their respective articles.

Refreshments will be served throughout the evening, and we hope that people will stay afterwards for our networking session over wine and bread.

*Venure provided by University of Copenhagen, Faculty of Science.

 

Past Events

We're delighted to invite our followers to visit Novozymes, world leader in biological solutions in Bagsværd. Novozymes is the branch of Novo A/S focusing on the production of industrial grade enzymes and microorganisms for consumer and manufaturers alike. At the moment, Novozymes are perhaps most famous for their development of heatstable enzymes for washing detergents, but they also dwell in sustainable energy and agricultural solutions.
The visit will involve a guided tour, lectures from department personal and data scientists as well as networking opportunities en masse. Refreshments are included.
For now, Novozymes have confirmed all bookings, and we look forward to welcoming you at their main building (8X), the address
is  Krogshøjvej 36, 2880 Bagsværd. It’s about a 10 minute walk from Bagsværd st., which is on S-train line A.
If you have further questions, you're more than welcome to message us on Facebook!

Date : 2 May 2017 at 18:00–21:00

Location : Seminar Room, 2nd floor ,Ole Maaløes Vej 5
The CBioVikings Pitch competition in collaboration with Computerome:
WIN UP TO 5000 COMPUTATION HOURS on Computerome as well as professional support to integrate your algorithm!
Top three will receive official diplomas from CBioVikings and Computerome, and featured on CBioVikings website.
You can win support and access to Computerome for any academic project with just 4 minutes presentation.
Who should participate?
Anyone who has been running code on their own laptop and wants to optimize, or who just want to run their code faster and better.
Open to BSc-, MSc-, PhD -students & Post Docs with an academic project.
Last year winners got assistance to run their code on Computerome, learn about their projects:
Peter Bork:
https://www.youtube.com/watch?v=5z7kT92JONE
Christian Ravn and Alexander Junge:
https://www.youtube.com/watch?v=xg79E2wY9Zk
Marisa Luisa Matey:
https://www.youtube.com/watch?v=K2WvRfQ8OjU
Computerome's present compute resources consist of 16048 CPU cores with 92 TeraBytes of memory, connected to 3 PetaBytes of High-performance storage, and with a total peak performance of more than 483 TeraFLOPS (483 million million floating-point operations per second). It debuted in November 2014 at #121 on TOP500 Supercomputing Sites within life science.
Sign up is only required for pitching.
Participants should sign up by emailing pitch@cbiovikings.org no later than April 27th at 18:00.
Requirements: You have max four minutes to give the pitch, and we need to have your slides on the day before the event in pdf format.
Beers and Chips will be available for refreshments.
We are very thankful for DeiC to support this event!

 

Date : 28 April 2017 at 18:00–20:00
Location : Studenterhuset (Købmagergade 52), Aquarium Room
Data comes in many forms, shapes and flavors. As tasty and free spirited as this may sound, the diligent data analyst often spends most of her/his time preparing and wrangling the data itself, rather than running or coding a particular model or statistical test. This is where Python and Pandas come into play, providing high-level, flexible, and efficient tools for manipulating your data as needed.
Program
CBioVikings will get a short introduction on how to use Jupyter Notebook (formerly IPython Notebook), an interactive computational environment, which combines code execution, rich text, mathematics, plots and media. Then we’ll delve right into Data Analysis using Pandas, a Python library providing easy-to-use data structures and data analysis tools.
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Date : 26 April at 18:00–20:00
Location : Seminar Room, 2nd floor ,Ole Maaløes Vej 5
 
We are pleased to announce the Annual CBioVikings General Assembly, where we elect a new board for everyone's favorite student organization. The board of 2017-18 will be in charge of organizing events and participating in conferences on behalf of CBioVikings during the next term, and it is an excellent opportunity for any student with interests within computational biology to join.
 
We welcome everybody with a curiosity related to any of our events to show up and meet with the people who has been organizing.
 
We love your feedback. and we would love to hear your ideas for potential events that we could host in the future.
 
This is also the event where we will elect new board members, so this is also a chance to support those with the ideas you like the most.
 
We also welcome new members to run for the board.
If it has your interest to be on the board we welcome you to send us an email to ask any questions you may have.
 
Beer and snacks will be served.
 
If you are interested in running for the board yourself, we are very happy to hear from you beforehand, in order to advise you which position may need your skills the most: info@cbiovikings.org you can also let us know on the day.
 
Looking forward to meet you.
https://www.facebook.com/events/1802706243280177/

Date: 2 February 2017, 17:30-20:00
Location: Studenterhuset
 
Presented By: Richard Röttger, Assistant Professor, Dr. rer. nat. at University of Southern Denmark in Odense.
 
Introduction
 
Equipped with sophisticated biochemical measurement techniques we generate a massive amount of biomedical data that needs to be analyzed computationally. One long-standing challenge in automatic knowledge extraction is clustering. We seek to partition a set of objects into groups such that the objects
within the clusters share common traits. In this workshop, a broad overview of a cluster analysis is given, from preprocessing, proximity calculation, the actual clustering to the evaluation of the results. We will have a particular emphasis on the various decisions a practitioner has to make and discuss the consequences on the clustering. Especially since a cluster analysis is often the very beginning of an entire analysis workflow, poor decisions may have severe consequence through the entire workflow.
 
Program
 
The workshop aims to raise this awareness and to equip the participants with according tools and strategies in order to produce high-quality and reliable clustering results. After the theoretical part, a hands-on tutorial will be conducted.
 
Prerequisites
 
Each participant should have their own laptop with them. Working in pairs is also fine. Please download and install R and RStudio to be able to follow along the presentation and participate in the workshop.

Date : 1 November at 17:00–20:00
Location : University of Copenhagen
 
The theme for this CBioVikings Symposium was Translational Bioinformatics, which is the field spanning healthcare, biomedical data and bioinformatics. Professor Søren Brunak introduced the field and the work in the Translational Disease Systems Biology group at University of Copenhagen.
 
We invited students and early career researchers within this field to present their work. This was a great opportunity to get feedback on their research and to practice presentation skills.
 
The symposium started at 17.00 and included drinks and food. It has been a fruitful evening with very nice discussions and networking opportunities. We thank everyone attended.
 
 
 
 
 

Galaxy Project Workshop

 

Date : 13 October at 18:00–21:00

Location : Studenterhuset, Købmagergade 52, 1150 København

Presented by: Jose Maria Gonzalez-Izarzugaza, Associate Professor at DTU and Alex Aguayo Orozco, PhD student at Center for Protein Research

 

Introduction

As the availability and amount of biological data becomes ever-increasing, it is important for one to know how to handle it and what tools to use to properly analyze it. This is where Galaxy Project comes into play, by providing easy to use, web-based platform for biomedical research. Galaxy Project is an open source framework for integrating various command line computational tools and databases into a cohesive workspace. The possible uses of Galaxy Project range from simple data format conversion to advanced NGS data analysis.

Program

CBioVikings gave a short summary on the basic uses of Galaxy Project in an interactive workshop manner. The workshop consisted of presentation and interactive exercises in groups consisting of 2-3 people, thus minimizing the server load.

 

 

Date: October 3rd 2016, 6pm

Location: Studenterhuset, Aquarium

Last year, we held a workshop called "Type Less and Do More on the Unix Command Line" that covered various features and commands to process data directly on the command line. This workshop "Type Even Less" was build on the previous, and gave attendants more techniques to help them work more efficiently.

We discussed how to use shell variables, how to run a sub process and use the result as input to another command, output redirection, how to redirect the output of two commands into a third (process substitution). These methods gave attendants more flexibility in constructing commands, and helped them to avoid writing temporary files so that they can get more done faster.

 
 
 
 
 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Date: April 21st 2016, 15:00-18:00
Location: Room A2-81.01 (3-01), Thorvaldsensvej 40, Frederiksberg, University of
Copenhagen, Denmark

Synopsis: This afternoon symposium gathered together researchers who are building and using open source tools to conduct reproducible science. We discussed the advantages and difficulties with this approach, and explored the best ways to implement it in practice.

The event was co-organized by IDA Biotechnology, the Danish Biotechnological Society (DBS) and CBioVikings - ISCB Regional Student Group Denmark. Event sponsors were intomics and Palantir.

Speakers

Kai Blin (Postdoc, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark) [pdf] [html]

Kai is an active contributor to many open source projects including Biopython and Samba, and is an advocate for open science approaches. His talk will discuss his personal approach to reproducible research.

Geoff Macintyre (Research Associate, Cambridge Cancer Center, University of Cambridge, UK) [pdf]

Geoff is a computational biologist who models tumor evolution. His talk will focus on concrete ways in which reproducible science benefits the careers of the researchers who implement it.

Sabarinathan Radhakrishnan (Biomedical Genomics Group, University Pompeu Fabra, Spain) [pdf]

Sabari studies the role of somatic mutations across different cancer types. In this talk he will focus on practical ways to enhance our research work by making it more transparent and reproducible.

Here is our full program.

Start time Title and Speaker
15:00 Welcome
Alexander Junge (CBioVikings)
15:05 Introduction
Helen Cook (CBioVikings)
15:20 Practice what you preach: reproducible research at the front lines of science
Kai Blin [pdf] [html]
15:50 Sponsor Talks
Palantir, Intomics
16:15 Break
16:40 Five selfish reasons to work reproducibly
Geoff Macintyre [pdf]
17:10 How to make our research work transparent and reproducible
Sabarinathan Radhakrishnan [pdf]
17:40 Closing
Jamshed Gill (CBioVikings)
17:45 Dinner
18:30 End

Why is reproducible research important to bioinformaticians?

It was reported last year that 50% of biomedical studies are not reproducible, and it may be the case that the percentage is even higher. The causes for not being able to reproduce research studies are numerous, but generally relate to a lack of documentation of materials, protocols, or study design. Regardless of the cause, the impacts of studies that cannot be verified are similar: they represent wasted funds and effort, and delay translation of research to the clinic.
Reproducible analyses help to avoid these problems, since they can be easily rerun and verified by reviewers or third parties, and shared between research groups. Further, conducting research with a focus on reproducibility also gives direct benefits to the researchers themselves. For example, results can be brought more quickly up to date with less chance of human errors, which enables continuity on long term projects. Ultimately this means that higher quality science can be done faster.
Since most bioinformatics analysis is done with computers, reproducibility initially seems like an easy goal to reach. However, in practice bioinformaticians face many barriers that prevent true reproducibility, such as versioning, data management, and documentation challenges. This symposium will focus on the tools that help overcome these challenges: languages like R and Python are used to script analyses, version control systems track changes between collaborators, documentation systems like knitR and Jupyter notebooks document analyses, and container systems like Docker deploy finished projects. Young researchers will learn how to implement these tools in their own research to the benefit of their own scientific development.
References:
http://whyopenresearch.org/
http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0850-7
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285

Sponsors


 
(Click the images to visit their website)

Coorganizers
 
 
 
 
 
 
 

When: March 5th 2016 at 12:00

Where: Conference room 1 (Upstairs), Building 101 entrance A, Anker Engelunds Vej 1, 2800 Kgs. Lyngby, DTU

In this CBioViking's symposium we focused on biological networks. There were three talks in various fields of network oriented research in biology by established researchers from different universities in Denmark. Before the talks, we organized a workshop on Cytoscape to sharpen participants' network analysis skills.

Snacks and drinks were be served during the event and there were plenty of opportunities for networking accompanied by beer for everyone.

We had around 50 participants and enjoyed a very productive Saturday afternoon together!

When: March 3rd 2016 at 18:00

Where: Studenterhuset - Aquarium

The CBioVikings Pitch competition in collaboration with Computerome:
Win up to 5000 computation hours on Computerome as well as professional support to integrate your algorithm!
Top three will receive official diplomas from CBioVikings and Computerome and be featured on CBioVikings website.
Who should participate?
Anyone who has been running code on their own laptop and wants to optimize, or who just want to run their code faster and better.
Open to BSc-, MSc-, PhD -students & Post Docs with an academic project.
Come and test out your pitching skills in a great audience!
Last year PhD student Emma Hagberg got assistance to run her code on Computerome, learn about her optimization here: https://www.youtube.com/watch?v=HPsWZzi5Gkg
Computerome's present compute resources consist of 16048 CPU cores with 92 TeraBytes of memory, connected to 3 PetaBytes of High-performance storage, and with a total peak performance of more than 483 TeraFLOPS (483 million million floating-point operations per second). It debuted in November 2014 at #121 on TOP500 Supercomputing Sites within life science.
Sign up is only required for pitching.
Participants should sign up by emailing pitch@cbiovikings.org no later than the first of Marc
Requirements: You have max four minutes to give the pitch, and we need to have your slides on the day before the event in pdf format.

Date/Time: December 3rd, 2015, 18:00
Location: Købmagergade 52, 1150 København K, Studenterhuset, Aquarium room
Speaker: Lars Roed Ingerslev, NNF-CBMR, KU
On this Viking Thursday we focused on how to generate high quality figures using the freely available R package ggplot2.
Figures are essential for summarizing and clearly communicating results to your peers. Thus every data scientist should be proficient in generating concise and easily interpreted figures. Multi-layered figures can easily be produced in the R environment with the ggplot2 package, and the clear grammar and vast flexibility of ggplot2 makes it simple to impose a common style on all your figures.
This was an "all levels" workshop, however, it was primarily aimed at people with a basic knowledge of R.

18:00 - 18:40 Interactive presentation

18:40 - 20:00 Group work, discussion and beverages
 
 
 
 
 
 
 

Date: November 21st 2015, 11:30-15:00

Location: Festauditoriet, Bulowsvej 17, Frederiksberg

This CBioViking's event was hosted with our collaborators IDA Biotechnology on the frontier research in cancer bioinformatics. There were four talks in various fields of cancer bioinformatics by established researchers from different universities in Denmark.

Program:
- Why haven’t we found a cure for cancer yet?
(Benito Campos, Heidelberg)
- Pan-cancer Analysis of Mutations in Non-coding Regulatory Regions (Jakob Skou Pedersen, AU)
- Decoding of Network Attacking Mutations Rewiring Cancer
(Rune Linding, KU)
- Genome-guided Cancer Diagnostics and Immunotherapy
(Aron Eklund, DTU)
A more detailed plan of the program is available here.
The event took place at the beautiful Festauditoriet in Frederiksberg. Food and drinks were served during the event and there were plenty of opportunities for networking.

The event was hosted by CBioVikings (ISCB Regional Student Group Denmark) and IDA Biotechnology.

OCTOBER 10th 2015, 12.00-16.30

COBIS, Ole Maaløes Vej 3, 2200 København N

Bioinformatics companies and startups face unique challenges as a result of spanning classic tech and biotech. These challenges relate especially to development of sustainable business models, data privacy laws and regulations, viable funding options, and a viable future.

At this event we explored the challenges faced by early stage bioinformatics companies, and the changing landscape within this rapidly expanding field. This was in the form of a number of talks and activities, which aimed to provoke the participants thoughts regarding these challenges, and to try and generate some solutions.

The started out with speakers from bioinformatics based companies and startups as well as representatives from the biotech innovation platform, COBIS. The former told their stories of how their organisations have developed from the ground up, some of the challenges they faced, and how they have overcome them. There was then a presentation from COBIS telling about how it is to start a company, and the benefits and challenges facing a company in Denmark.

The day finished with a workshop for generating ideas for new bioinformatics companies and where we tried to get to the bottom of the challenges facing commercialization of bioinformatics and strategies for how these challenges can be negotiated.

Date: October 1st 2015, 6pm

Location: Studenterhuset, Church wing

One of the skills that is most fundamental to bioinformatics is the proficient use of the unix command line.

Many common data manipulation tasks can of course be accomplished by writing a small program, but there is also a plethora of unix tools available that can accomplish the same results with less keystrokes.

Having a large toolbox gives you more flexibility, and will save you from reinventing the wheel.

On this Viking Thursday, we discussed how to make the command line work for you, and how to get more done while typing less.

This was an "all levels" workshop, though it was primarily aimed at people who know how to navigate around the unix shell, but who aren't yet very comfortable there.

6:00 - 6:45 Interactive presentation

6:45 - 8:00 Discussion and beverages

VIRUS SYMPOSIUM (JUNE 2015)

EFFICIENT PROGRAMMING WORKSHOP
(MAY 2015)
On 5 May 2015, we have organised a workshop about efficient programming where we focused on 3 main topics; version control with GIT, algorithm design paradigms and unit testing in Python.
Our CBioVikings board members, Alexander Junge, Ferhat Alkan and Helen Cook hosted the workshop in Studenterhuset by giving presentations and sharing their experiences with around 50 participants. With hands-on exercises and active participation of attendees, followed by beer session afterwards, it has been a joyful night for everyone.

BIOINFORMATIC CHARADES (MARCH 2015)

THE WORLD of 3D (FEBRUARY 2015)
The first academic event by CBioVikings took place in the professional settings of DTU building 101 in the end of February 2015. It was co-organized with IDA Biotechnology and the Danish Biotechnological Society. More than 70 people had shown up to witness the opening of the event with CBioVikings Advisor, Professor José MG Izarzugaza(DTU), followed by Professor Thomas Frimurer(UCPH) who gave the first CBioVikings Lecture, and Professor Ingemar André(LU) as the first international speaker. At the event we had 3D printed model proteins related to the subject of the speakers with the help of DTU Skylab. A short presentation about the Danish Elixir Node was given as well as two SpaceNavigator® sponsored by the company 3Dconnexion, were awarded as prizes for providing feedback on the event. Following the event was food and networking with a beer.

VOLUNTEER SPEED DATING (FEBRUARY 2015)
The first CBioVikings social event on February 10th 2015 was to meet each other with a bit of fun through scientific speed dating.
Everyone was paired with everyone else in turn, so that we generated a fully connected conversation graph. During each 5 minute conversation, we had a chance to present ourselves and our research, to discover shared scientific interests, and to talk about the ways we would like to be involved with CBioVikings in the future.
In all, 14 people attended, and it was a good way to be introduced to other bioinformaticians in our community.

GALLERY OF PICTURES
KICK-OFF EVENT (DECEMBER 2014)
The kick-off meeting was the first event organized by CBioVikings. With this event we wanted to introduce the group, our objectives, ideas and our vision of what a group like this could bring to the computational biology field in Denmark. This meeting had also the objective to have a feeling of the acceptance of this initiative and get to know students and young scientist interested in participating as volunteers. The event was a blast! Many people attended the event and we had very good feedback that clearly showed the demand for a group like this and where we recruited many volunteers that have helped ever since in all the events hosted by CBioVikings, ISCB Regional Student Group in Denmark.